My experiment has two factors, binary and continuous variables.
The normality test gave p
Dear Isadora Moreira da Luz Real,
Please fined a reply I found related to your query.
your question was very relevant, and it seems that many people have the same problem, according to the many views. The function I posted is now in use by many people, but once in a while I get a message from somebody claiming that the function is returning an error. I made some debugging to the original function and added to possibility to use dissimilarities generated by 'daisy' from package 'cluster' rather that 'vegdist' from 'vegan'. You can find this function if you browse to all the posts, but my first answer was voted by many people, so it appears first.
So, It is very important that everybody of you vote to this answer here, were I am posting again the final function (below). Please use only this function.
To use the function. Read the header of the file below.
You can just copy&paste the content of the file to your running R session.
The use like this:
data(iris)
pairwise.adonis(iris[,1:4],iris$Species)
more examples in the file below.
enjoy, Pedro
also look at this.
It happens that I had the same problem, and google didn't gave me any solution.
I took up the comment of Martin to program a function for pairwise adonis using subsets of the dataset. You will find the function below. After copy-pasting the code below into your R session, you will be able to use the function pairwise.adonis() with following arguments
x = the community table
factors = a column or vector with all factors to be tested pairwise
sim.method = similarity function, one of the functions available in vegdist(); default is 'bray' for bray-curtis
p.adjust.m = the p.value correction method, one of the methods supported by p.adjust(); default is 'bonferroni'
The function will return a table with the pairwise factors, F-values, R^2, p.value and adjusted p.value
Regards Pedro
##start copy here for function pairwise.adonis()
pairwise.adonis
Please install the function from Github. It has been updated.
https://github.com/pmartinezarbizu/pairwiseAdonis
Pedro
- Badges
- Science topic
- Similar topics
- Biological Science
- Kinesiology
- Running